/*
 * Licensed to the Apache Software Foundation (ASF) under one or more
 * contributor license agreements.  See the NOTICE file distributed with
 * this work for additional information regarding copyright ownership.
 * The ASF licenses this file to You under the Apache License, Version 2.0
 * (the "License"); you may not use this file except in compliance with
 * the License.  You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package org.apache.tika.parser.isatab;

import java.io.IOException;
import java.io.InputStream;
import java.io.Reader;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Locale;
import java.util.Map;

import org.apache.commons.csv.CSVFormat;
import org.apache.commons.csv.CSVParser;
import org.apache.commons.csv.CSVRecord;
import org.apache.commons.io.input.CloseShieldInputStream;
import org.xml.sax.SAXException;

import org.apache.tika.config.TikaConfig;
import org.apache.tika.detect.AutoDetectReader;
import org.apache.tika.detect.DefaultEncodingDetector;
import org.apache.tika.detect.EncodingDetector;
import org.apache.tika.exception.TikaException;
import org.apache.tika.io.TikaInputStream;
import org.apache.tika.metadata.Metadata;
import org.apache.tika.parser.ParseContext;
import org.apache.tika.sax.XHTMLContentHandler;

public class ISATabUtils {

    /**
     * INVESTIGATION
     */

    // Investigation section.
    private static final String[] sections =
            {"ONTOLOGY SOURCE REFERENCE", "INVESTIGATION", "INVESTIGATION PUBLICATIONS",
                    "INVESTIGATION CONTACTS"};

    // STUDY section (inside the Study section)
    private static final String studySectionField = "STUDY";

    // Study File Name (inside the STUDY section)
    private static final String studyFileNameField = "Study File Name";

    public static void parseInvestigation(InputStream stream, XHTMLContentHandler handler,
                                          Metadata metadata, ParseContext context,
                                          String studyFileName)
            throws IOException, TikaException, SAXException {

        // Automatically detect the character encoding
        try (AutoDetectReader reader = new AutoDetectReader(CloseShieldInputStream.wrap(stream),
                metadata)) {
            extractMetadata(reader, metadata, studyFileName);
        }
    }

    public static void parseInvestigation(InputStream stream, XHTMLContentHandler handler,
                                          Metadata metadata, ParseContext context)
            throws IOException, TikaException, SAXException {
        parseInvestigation(stream, handler, metadata, context, null);
    }

    public static void parseStudy(InputStream stream, XHTMLContentHandler xhtml, Metadata metadata,
                                  ParseContext context)
            throws IOException, TikaException, SAXException {
        TikaInputStream tis = TikaInputStream.get(stream);
        // Automatically detect the character encoding
        EncodingDetector encodingDetector = getEncodingDetector(context);
        try (AutoDetectReader reader = new AutoDetectReader(CloseShieldInputStream.wrap(tis),
                metadata, encodingDetector);
                CSVParser csvParser = CSVParser.builder().setReader(reader).setFormat(CSVFormat.TDF).get()) {
            Iterator<CSVRecord> iterator = csvParser.iterator();

            xhtml.startElement("table");

            xhtml.startElement("thead");
            if (iterator.hasNext()) {
                CSVRecord record = iterator.next();
                for (int i = 0; i < record.size(); i++) {
                    xhtml.startElement("th");
                    xhtml.characters(record.get(i));
                    xhtml.endElement("th");
                }
            }
            xhtml.endElement("thead");

            xhtml.startElement("tbody");
            while (iterator.hasNext()) {
                CSVRecord record = iterator.next();
                xhtml.startElement("tr");
                for (int j = 0; j < record.size(); j++) {
                    xhtml.startElement("td");
                    xhtml.characters(record.get(j));
                    xhtml.endElement("td");
                }
                xhtml.endElement("tr");
            }
            xhtml.endElement("tbody");

            xhtml.endElement("table");
        }
    }

    private static EncodingDetector getEncodingDetector(ParseContext context) {
        TikaConfig tikaConfig = context.get(TikaConfig.class);
        if (tikaConfig != null) {
            return tikaConfig.getEncodingDetector();
        }
        return new DefaultEncodingDetector();
    }

    public static void parseAssay(InputStream stream, XHTMLContentHandler xhtml, Metadata metadata,
                                  ParseContext context)
            throws IOException, TikaException, SAXException {
        TikaInputStream tis = TikaInputStream.get(stream);

        // Automatically detect the character encoding
        EncodingDetector encodingDetector = getEncodingDetector(context);
        try (AutoDetectReader reader = new AutoDetectReader(CloseShieldInputStream.wrap(tis),
                metadata, encodingDetector);
                CSVParser csvParser = CSVParser.builder().setReader(reader).setFormat(CSVFormat.TDF).get()) {
            xhtml.startElement("table");

            Iterator<CSVRecord> iterator = csvParser.iterator();

            xhtml.startElement("thead");
            if (iterator.hasNext()) {
                CSVRecord record = iterator.next();
                for (int i = 0; i < record.size(); i++) {
                    xhtml.startElement("th");
                    xhtml.characters(record.get(i));
                    xhtml.endElement("th");
                }
            }
            xhtml.endElement("thead");

            xhtml.startElement("tbody");
            while (iterator.hasNext()) {
                CSVRecord record = iterator.next();
                xhtml.startElement("tr");
                for (int j = 0; j < record.size(); j++) {
                    xhtml.startElement("td");
                    xhtml.characters(record.get(j));
                    xhtml.endElement("td");
                }
                xhtml.endElement("tr");
            }
            xhtml.endElement("tbody");

            xhtml.endElement("table");
        }
    }

    private static void extractMetadata(Reader reader, Metadata metadata, String studyFileName)
            throws IOException {
        boolean investigationSection = false;
        boolean studySection = false;
        boolean studyTarget = false;

        Map<String, String> map = new HashMap<>();

        try (CSVParser csvParser = CSVParser.builder().setReader(reader).setFormat(CSVFormat.TDF).get()) {

            for (CSVRecord record : csvParser) {
                String field = record.get(0);
                if ((field.toUpperCase(Locale.ENGLISH).equals(field)) && (record.size() == 1)) {
                    investigationSection = Arrays.asList(sections).contains(field);
                    studySection = (studyFileName != null) && (field.equals(studySectionField));
                } else {
                    if (investigationSection) {
                        addMetadata(field, record, metadata);
                    } else if (studySection) {
                        if (studyTarget) {
                            break;
                        }
                        String value = record.get(1);
                        map.put(field, value);
                        studyTarget =
                                (field.equals(studyFileNameField)) && (value.equals(studyFileName));
                        if (studyTarget) {
                            mapStudyToMetadata(map, metadata);
                            studySection = false;
                        }
                    } else if (studyTarget) {
                        addMetadata(field, record, metadata);
                    }
                }
            }
        } catch (IOException ioe) {
            throw ioe;
        }
    }

    private static void addMetadata(String field, CSVRecord record, Metadata metadata) {
        if ((record == null) || (record.size() <= 1)) {
            return;
        }

        for (int i = 1; i < record.size(); i++) {
            metadata.add(field, record.get(i));
        }
    }

    private static void mapStudyToMetadata(Map<String, String> map, Metadata metadata) {
        for (Map.Entry<String, String> entry : map.entrySet()) {
            metadata.add(entry.getKey(), entry.getValue());
        }
    }
}
